Single Particle Orientation and Rotational Tracking

ABSTRACTPreferred particle orientation represents a recurring problem in single-particle cryogenic electron microcopy (cryo-EM). A specimen-independent approach through tilting has been attempted to increase particle orientation coverage, thus minimizing anisotropic three-dimensional (3D) reconstruction. However, focus gradient is a critical issue hindering tilt applications from being a general practice in single-particle cryo-EM. The present study describes a newly developed geometrically optimized approach, goCTF, to reliably determine the global focus gradient. A novel strategy of determining contrast transfer function (CTF) parameters from a sector of the signal preserved power spectrum is applied to increase reliability. Subsequently, per-particle based local focus refinement is conducted in an iterative manner to further improve the defocus accuracy. Novel diagnosis methods using a standard deviation defocus plot and goodness fitting heatmap have also been proposed to evaluate CTF fitting quality prior to 3D refinement. In a benchmark study, goCTF processed a published single-particle cryo-EM dataset for influenza hemagglutinin trimer collected at a 40-degree specimen tilt. The resulting 3D reconstruction map was improved from 4.1Å to 3.7Å resolution. The goCTF program is built on the open-source code of CTFFIND4, which adopts a consistent user interface ease of use.

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The microwave properties of simulated melting precipitation particles: sensitivity to initial melting

Atmospheric Measurement Techniques ◽

10.5194/amt-9-9-2016 ◽

2016 ◽

Vol 9 (1) ◽

pp. 9-21 ◽

Cited By ~ 12

Author(s):

B. T. Johnson ◽

W. S. Olson ◽

G. Skofronick-Jackson

Keyword(s):

Single Particle ◽

Microwave Remote Sensing ◽

Dipole Approximation ◽

Variable Density ◽

Particle Orientation ◽

Liquid Volume ◽

Simplified Approach ◽

Microwave Brightness Temperature ◽

Initial Melting ◽

Global Precipitation

Abstract. A simplified approach is presented for assessing the microwave response to the initial melting of realistically shaped ice particles. This paper is divided into two parts: (1) a description of the Single Particle Melting Model (SPMM), a heuristic melting simulation for ice-phase precipitation particles of any shape or size (SPMM is applied to two simulated aggregate snow particles, simulating melting up to 0.15 melt fraction by mass), and (2) the computation of the single-particle microwave scattering and extinction properties of these hydrometeors, using the discrete dipole approximation (via DDSCAT), at the following selected frequencies: 13.4, 35.6, and 94.0 GHz for radar applications and 89, 165.0, and 183.31 GHz for radiometer applications. These selected frequencies are consistent with current microwave remote-sensing platforms, such as CloudSat and the Global Precipitation Measurement (GPM) mission. Comparisons with calculations using variable-density spheres indicate significant deviations in scattering and extinction properties throughout the initial range of melting (liquid volume fractions less than 0.15). Integration of the single-particle properties over an exponential particle size distribution provides additional insight into idealized radar reflectivity and passive microwave brightness temperature sensitivity to variations in size/mass, shape, melt fraction, and particle orientation.

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